As erratic rainfall and flooding pose serious threats to rice yields, submergence tolerance is critical for sustainable cultivation. This study screened 250 Indian rice landraces at the seedling stage to identify genotypes capable of surviving submergence stress. Advanced statistical analyses, including trait association, variability, principal component analysis and cluster analysis, revealed the genetic and phenotypic factors influencing submergence stress tolerance. Significant variability was observed among the genotypes for key traits, such as shoot elongation, leaf regeneration and survival percentage. Diversity analysis through cluster analysis indicated that cluster III, particularly IRGC93, IRGC535 and IRGC706, exhibited survival rates exceeding 85%, highlighting their potential as donor lines for submergence tolerance. Further biochemical analysis of selected lines with survival percentages greater than 50% revealed that tolerance is associated with greater chlorophyll and non-structural carbohydrate retention percentages. The findings emphasize the importance of genetic variability and heritability in breeding resilient rice varieties for flash flooding conditions. This research contributes to advancing rice breeding strategies to produce submergence-tolerant varieties, thereby promoting the sustainability and productivity of paddy production systems.